Neovascular glaucoma (NVG) is a secondary glaucoma with a poor visual prognosis. Trabeculectomy with antifibrotic agents, glaucoma drainage devices (GDDs), and cyclo-destructive procedures are recommended in patients who are refractory to medical management. However, due to the poor success rate of conventional trabeculectomy and the higher cost of GDDs, alternative procedures need to be looked at. To compare the surgical outcomes and economic aspects of a newly developed polypropylene suture bed-based modified trabeculectomy to Ahmed glaucoma valve (AGV) implantation for NVG. It was a prospective interventional study conducted at a tertiary care center between 2018 and 2020. Consecutive patients with NVG with a minimum follow-up of 18 months were included. Surgical outcomes are mainly based on intraocular pressure (IOP) control and the cost of surgery. Sixty eyes were included out of which 40 (60.6%) underwent modified trabeculectomy and 20 (33.7%) underwent AGV. At the final follow-up, no significant difference (P < 0.05) was found between the surgical outcomes of both groups. The complete success rate (IOP < 21 mm Hg without antiglaucoma medications) was 60 and 65% while the qualified success rate (IOP < 21 mm Hg with antiglaucoma medications) was 30 and 25% in modified trabeculectomy and AGV groups, respectively, at final follow-up. The cost of surgery was significantly higher in the AGV group (P < 0.0001). Modified trabeculectomy as described might be a better alternative for NVG eyes.